Up. Crystals of the native protein were obtained in 100 mM sodium acetate pH 5.0, 100 mM CaCl2 and 20 PEG4000. Crystals of the SeMet containing protein were obtained in the same conditions after seeding with the native crystals.Conserved or Polymorphic FimP and FimA Features among Clinical A. oris IsolatesSequencing of the fimP gene from six A. oris reference strains (T14V, PK1259, P-1-N, P-8-L, LY7 and P-1-K) expressing FimP pili of defined binding profiles [39,40] and clinical isolates (n = 42) revealed a highly conserved (97 identity/98 similarity) sequence (Fig. 6a). All three isopeptide bond triads, the cysteine bridges, pilin and LPLTG PTH 1-34 web Chebulagic acid motifs were fully, and the metal binding loop highly, conserved among the strains (n = 48). The variable or polymorphic amino acid sites (19 ), which localized generally over the domains, loops and b-strands without any apparent clustering or patterning, generated a total of sixteen allelic or sequence types (Fig. 6c). FimP was also compared to FimA, deduced from fimA from A. oris isolates (n = 14). The FimP and FimA proteins showed 31 identity/45 similarity and fully conserved isopeptide bond triads, number of cysteines, pilin and LPLTG motifs. The metal binding loop was proved to be unique for FimP and the proline-richGeneration of Isopeptide Bond MutantsGeneration of the mutants D230A and E452A was performed using the overlap extension PCR technique [41]. In short, for each mutant a first round of PCR generated two overlapping PCR fragments. In the second PCR step the two fragments were hybridized and amplified. The final PCR products were ligatedFimP Structure and Sequence AnalysesFigure 6. Sequence analyses of FimP and FimA among A. oris isolates. A: Sequence alignment of FimP (n = 48) with fully conserved isopeptide bond triads (red), disulfide bonds (green), a conserved metal binding loop (grey) and pilin-, E-box- and LPLTG motifs in yellow. B: Sequence alignment of FimA (n = 14) with fully conserved 1676428 isopeptide bond triads (red), disulfide bonds (green), a conserved proline-rich loop (blue) and pilin-, E-box- and LPLTG motifs in yellow. In addition, in A and B, polymorphic amino acid residues are shown (single letter codes). The top lines represent the consensus sequence and amino acid positions based on FimP and FimA respectively of reference strain T14V. C: Neighboring joining tree with sixteen allelic or sequence fimP types among A. oris isolates (n = 48) due to the single amino acid variations. doi:10.1371/journal.pone.0048364.ginto 24786787 an expression vector as described [31]. The mutant proteins were purified as the native protein.Mass Spectrometry AnalysesBuffer solutions of FimP, FimP-D230A, and FimP-E452A were exchanged for water by dialysis. Accurate molecular masses were determined by ESI-TOF mass spectrometry at Proteomics Karolinska (PK) Institute, Stockholm, Sweden.Data Collection and Structure DeterminationCrystals were flash-cooled in liquid nitrogen after a 30 s soak in the crystallization solution supplemented with 20 glycerol. X-ray diffraction data of the native crystals were collected at beamline ID14-1 and of the SeMet crystals at beamline ID-23 at the European Synchrotron Radiation Facility, ESRF, in Grenoble, ?France to 1.6 and 2.0 A resolution respectively. Data were processed with XDS [42] and scaled with SCALA from the CCP4 program suit [33]. The SeMet containing structure was solved with SAD-phasing using AutoRickshaw [43]. Density modification and automatic model.Up. Crystals of the native protein were obtained in 100 mM sodium acetate pH 5.0, 100 mM CaCl2 and 20 PEG4000. Crystals of the SeMet containing protein were obtained in the same conditions after seeding with the native crystals.Conserved or Polymorphic FimP and FimA Features among Clinical A. oris IsolatesSequencing of the fimP gene from six A. oris reference strains (T14V, PK1259, P-1-N, P-8-L, LY7 and P-1-K) expressing FimP pili of defined binding profiles [39,40] and clinical isolates (n = 42) revealed a highly conserved (97 identity/98 similarity) sequence (Fig. 6a). All three isopeptide bond triads, the cysteine bridges, pilin and LPLTG motifs were fully, and the metal binding loop highly, conserved among the strains (n = 48). The variable or polymorphic amino acid sites (19 ), which localized generally over the domains, loops and b-strands without any apparent clustering or patterning, generated a total of sixteen allelic or sequence types (Fig. 6c). FimP was also compared to FimA, deduced from fimA from A. oris isolates (n = 14). The FimP and FimA proteins showed 31 identity/45 similarity and fully conserved isopeptide bond triads, number of cysteines, pilin and LPLTG motifs. The metal binding loop was proved to be unique for FimP and the proline-richGeneration of Isopeptide Bond MutantsGeneration of the mutants D230A and E452A was performed using the overlap extension PCR technique [41]. In short, for each mutant a first round of PCR generated two overlapping PCR fragments. In the second PCR step the two fragments were hybridized and amplified. The final PCR products were ligatedFimP Structure and Sequence AnalysesFigure 6. Sequence analyses of FimP and FimA among A. oris isolates. A: Sequence alignment of FimP (n = 48) with fully conserved isopeptide bond triads (red), disulfide bonds (green), a conserved metal binding loop (grey) and pilin-, E-box- and LPLTG motifs in yellow. B: Sequence alignment of FimA (n = 14) with fully conserved 1676428 isopeptide bond triads (red), disulfide bonds (green), a conserved proline-rich loop (blue) and pilin-, E-box- and LPLTG motifs in yellow. In addition, in A and B, polymorphic amino acid residues are shown (single letter codes). The top lines represent the consensus sequence and amino acid positions based on FimP and FimA respectively of reference strain T14V. C: Neighboring joining tree with sixteen allelic or sequence fimP types among A. oris isolates (n = 48) due to the single amino acid variations. doi:10.1371/journal.pone.0048364.ginto 24786787 an expression vector as described [31]. The mutant proteins were purified as the native protein.Mass Spectrometry AnalysesBuffer solutions of FimP, FimP-D230A, and FimP-E452A were exchanged for water by dialysis. Accurate molecular masses were determined by ESI-TOF mass spectrometry at Proteomics Karolinska (PK) Institute, Stockholm, Sweden.Data Collection and Structure DeterminationCrystals were flash-cooled in liquid nitrogen after a 30 s soak in the crystallization solution supplemented with 20 glycerol. X-ray diffraction data of the native crystals were collected at beamline ID14-1 and of the SeMet crystals at beamline ID-23 at the European Synchrotron Radiation Facility, ESRF, in Grenoble, ?France to 1.6 and 2.0 A resolution respectively. Data were processed with XDS [42] and scaled with SCALA from the CCP4 program suit [33]. The SeMet containing structure was solved with SAD-phasing using AutoRickshaw [43]. Density modification and automatic model.
